SMTL ID : 3ogw.1

Structure of the complex of bovine lactoperoxidase with indomethacin at 1.9A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.217 NAG-NAG.2: 3 residues within 4Å: Chain A: N.332, S.334, V.335 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.110, T.184, F.186, D.188, S.190 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.110, A:D.110, A:T.184, A:F.186, A:S.190

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: H.222, H.558 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.222, A:H.558, H2O.20

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 24 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.18, IMN.22 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, A:Q.259, A:F.347, A:F.347, A:F.347, A:R.348, A:V.354, A:F.380, A:L.417, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Water bridges: A:F.113, A:R.348, A:R.348, A:R.348, A:R.348, A:R.440 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 2 residues within 4Å: Chain A: N.95, I.315 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 Water bridges: A:N.95, A:R.96, A:R.96 NAG.7: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.244 Water bridges: A:N.382, A:R.385

14 x IOD: IODIDE ION(Non-functional Binders)

IOD.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: R.96, R.506 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: E.363, Y.365, R.397, T.560 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: R.31 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: S.359 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: P.375, H.377, K.420 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: H.109, R.255 Ligands: HEM.5, IMN.22 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: N.216, F.229 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP

1 x IMN: INDOMETHACIN(Non-covalent)

IMN.22: 13 residues within 4Å: Chain A: Q.105, H.109, F.113, P.115, E.116, F.254, R.255, E.258, F.381, Q.423 Ligands: HEM.5, IOD.18, SCN.25 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.255, A:R.255, A:E.258, A:E.258, A:F.381 Hydrogen bonds: A:E.116 Water bridges: A:Q.423, A:Q.423

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.23: 4 residues within 4Å: Chain A: S.198, L.199, R.202, F.254 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.199 MPD.24: 4 residues within 4Å: Chain A: T.23, I.24, T.25, P.197 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.24, A:P.197 Hydrogen bonds: A:I.24

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.25: 5 residues within 4Å: Chain A: N.230, C.248, F.254, F.381 Ligands: IMN.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.254

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.26: 4 residues within 4Å: Chain A: L.224, A.225, R.271, R.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.225 Water bridges: A:R.278, A:N.556 EDO.27: 4 residues within 4Å: Chain A: S.451, Q.460, K.462, D.488 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.462 Water bridges: A:N.68, A:S.451, A:S.451, A:S.451, A:D.488

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 4 residues within 4Å: Chain A: M.501, V.502, R.504, R.506 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.501, A:R.504, A:R.506 Water bridges: A:M.501, A:R.506 GOL.29: 6 residues within 4Å: Chain A: R.204, N.205, L.206, S.208, G.289, E.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.205, A:G.289, A:E.290 Water bridges: A:N.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, N. et al., Structure of the complex of bovine lactoperoxidase with indomethacin at 1.9A resolution. To be Published

Release Date

2010-12-01

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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